Figure 1. Length Frequencies with age modes (red) and total distributions (green) from the statistical estimation overlayed.

Figure 2. Deterministic numbers-at-age from age slicing procedure.

Figure 3. Statistical estimates of numbers-at-age from the mixture distribution analysis.

Figure 4. A comparison of catch numbers-at-age from the statistical and deterministic ageing procedures.

Figure 5. Standardised residuals of the proportion of numbers-at-age from the deterministic age slicing procedure (red negative and black positive residuals).

Figure 6. Standardised residuals for the proportion of numbers-at-age from the statistical mixture distribution analysis (red negative and black positive residuals).

Figure 7. Comparison of total catch biomass derived from different procedures.

[1] 1.018803

Figure 8. Catch-at-size by lustrum (5 year block).

Figure 9. Powell-Wheatherall plots

Figure 10. Estimates of Z derived from the Powell-Wetherall plots; showing the estimates from each year (black line with points) and a smoother (blue continuous line).

Figure 11. Catch curves by lustrum from statisical age estimates.

Figure 12. Estimated selectivity by lustrum.

Selectivity by gear

Figure 13. Catch curves by gear based on age estimates

Selectivity by gear and lustrum

Figure 14. Catch curves by gear and lustrum based on statistical age estimates.

XSA Continuity Run

Figure 15. XSA diagnostics from continuity run; residuals against fitted value.

Figure 16. XSA diagnostics from continuity run; residuals against year.

Figure 17. XSA diagnostics from continuity run; Calibration regression plots for age 2 (outlier for Scilian gillnet removed).

Figure 18. XSA diagnostics from continuity run; Calibration regression plots for age 3 (outlier for Scilian gillnet removed).

Figure 19. XSA diagnostics from continuity run; Calibration regression plots for age 4 (outlier for Scilian gillnet removed).

Figure 20. XSA diagnostics from continuity run; AR plots of lagged residuals

Figure 21. XSA diagnostics from continuity run; QQ plots to check for normality

Figure 22. XSA diagnostics from continuity run; weights for terminal year Ns for each CPUE observation and shrinkage

Figure 23. XSA time series estimates by CPUE series.

Figure 24. Retrospective XSA time series estimates.

Alternative Run

Figure 25. XSA diagnostics from alternative run; residuals against fitted value.

Figure 26. XSA diagnostics from from alternative run; residuals against year.

Figure 27. XSA diagnostics from from alternative run; Calibration regression plots for age 2.

Figure 28. XSA diagnostics from alternative run; Calibration regression plots for age 3.

Figure 29. XSA diagnostics from alternative run; Calibration regression plots for age 4.

Figure 30. XSA diagnostics alternative run; AR plots of lagged residuals

Figure 31. XSA diagnostics alternative run; QQ plots to check for normality

Figure 32. XSA diagnostics alternative run; weights for terminal year Ns for each CPUE observation and shrinkage

Figure 33. XSA time series estimates by CPUE series.

Figure 34. Retrospective XSA time series estimates.

Stock Status

Figure 35. XSA alternative run.

Stock Status

Figure 36. Stock Recruitment Relationship

[1] TRUE

Figure 37a. Equilibrium Analysis with reference points.

Figure 37b. Equilibrium Analysis with observations.

Figure 38. Kobe Phase Plot.

Figure 39. Current and mesopelagic selection patterns.

Figure 40. Projections for current selection pattern.

Figure 41. Projections for 50:50 current:mesopelagic selection pattern.

Tables

Table 1a. XSA Control options from continuity run.

tol          1e-09 
maxit        30 
min.nse          0.3 
fse          0.3 
rage         1 
qage         6 
shk.n        TRUE 
shk.f        TRUE 
shk.yrs          5 
shk.ages         5 
window       100 
tsrange          20 
tspower          3 
vpa          TRUE 

Table 1b. XSA Control options from alternative run.

tol          1e-09 
maxit        30 
min.nse          0.3 
fse          0.5 
rage         1 
qage         6 
shk.n        TRUE 
shk.f        TRUE 
shk.yrs          5 
shk.ages         1 
window       100 
tsrange          20 
tspower          3 
vpa          TRUE 

Table 2a. Reference Points

An object of class "FLPar"
        quantity
refpt    harvest    yield      rec        ssb        biomass   
  virgin 0.0000e+00 0.0000e+00 8.7253e+02 2.3996e+05 2.7087e+05
  msy    2.3716e-01 1.5822e+04 8.7239e+02 4.9001e+04 7.2683e+04
  crash  3.0960e+00 2.0528e-03 2.5897e-04 2.9679e-06 1.4372e-03
  f0.1   1.4443e-01 1.4864e+04 8.7247e+02 8.3994e+04 1.1018e+05
  fmax   2.3729e-01 1.5822e+04 8.7239e+02 4.8968e+04 7.2647e+04
  spr.30 1.6967e-01 1.5377e+04 8.7245e+02 7.1982e+04 9.7449e+04
units:  NA 

Table 2b. Reference Points with 50% Mesopelagic selection pattern.

An object of class "FLPar"
        quantity
refpt    harvest    yield      rec        ssb        biomass   
  virgin 0.0000e+00 0.0000e+00 8.7253e+02 2.3996e+05 2.7087e+05
  msy    2.3936e-01 1.6928e+04 8.7239e+02 4.8014e+04 7.3028e+04
  crash  3.6667e+00 2.3426e-03 2.6828e-04 3.0746e-06 1.7894e-03
  f0.1   1.3890e-01 1.5797e+04 8.7247e+02 8.4891e+04 1.1215e+05
  fmax   2.3950e-01 1.6928e+04 8.7239e+02 4.7980e+04 7.2991e+04
  spr.30 1.6610e-01 1.6410e+04 8.7245e+02 7.1982e+04 9.8604e+04
units:  NA 

Table 3. Stock information

An object of class "FLStock"
Slot "catch":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985  1986  1987  1988  1989  1990  1991  1992  1993  1994  1995 
  all 15292 16765 18320 20365 17762 16018 15746 14709 13265 16082 13015
     year
age   1996  1997  1998  1999  2000  2001  2002  2003  2004  2005  2006 
  all 12053 14693 14369 13699 15569 15006 12814 15674 14405 14601 14893
     year
age   2007  2008  2009  2010  2011  2012  2013 
  all 14227 12164 11840 13430 11423  9888 11254

units:  NA 

Slot "catch.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985    1986    1987    1988    1989    1990    1991    1992   
  0  28.242  23.026  59.863  87.583  85.120  24.241  37.785  64.576
  1 136.249  97.223 143.828 251.937 198.807 245.874 174.984 183.301
  2 123.464 164.965 122.299 154.170 158.743 264.890 183.578 199.169
  3  80.758  79.100  82.774  87.777  90.329  78.250  95.343  64.861
  4  43.094  44.479  61.249  66.955  55.246  24.141  35.914  30.297
  5  51.689  60.082  68.676  61.586  45.683  23.961  32.666  33.308
   year
age 1993    1994    1995    1996    1997    1998    1999    2000   
  0  57.788  68.150  68.078  37.792  33.533  58.288  37.498  17.538
  1 250.042 215.968 244.803 179.192 158.290 246.861 179.594 211.476
  2 176.138 224.500 153.038 149.822 184.718 146.685 144.680 169.683
  3  51.152  70.369  56.648  68.404  88.963  58.984  69.426  80.395
  4  23.242  26.086  22.841  22.853  39.951  32.727  35.523  37.796
  5  27.114  36.020  26.344  21.687  24.210  39.081  33.797  37.307
   year
age 2001    2002    2003    2004    2005    2006    2007    2008   
  0  28.657  19.958  58.022  66.847  19.269  33.028  27.082  15.925
  1 197.246 299.699 227.069 248.912 238.277 174.597 276.103 286.693
  2 185.113 190.989 244.351 162.812 182.680 178.085 147.444 163.687
  3  84.975  48.805  78.228  68.060  67.495  63.710  69.903  61.353
  4  29.106  17.499  29.984  31.323  28.467  30.916  31.339  21.385
  5  29.979  20.505  21.683  31.797  30.265  39.870  28.437  14.084
   year
age 2009    2010    2011    2012    2013   
  0  13.939  30.301  93.302  24.092   4.295
  1 190.718 155.590 127.894 119.511 138.311
  2 140.944 125.927 119.679  85.382 147.900
  3  59.636  82.183  75.960  44.170  53.653
  4  32.426  42.514  24.176  20.804  24.865
  5  21.934  29.184  22.413  26.463  25.440

units:  NA 

Slot "catch.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0   3.6532   3.4611   4.1852   4.7990   3.5240   3.5432   3.5686
  1  11.3859  11.4094  10.7864  10.9208  11.4493  11.3028  11.4519
  2  23.2197  23.5354  23.5257  22.7368  22.6423  23.1079  23.4560
  3  39.8577  39.8580  39.8599  40.2500  39.9222  39.8653  40.0094
  4  59.3496  59.6720  60.0047  59.5889  59.7872  59.4888  59.4173
  5  92.3146  93.0339  93.7232  95.3473  95.1656  92.8173  96.0019
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0   3.5737   3.7333   3.6320   3.5368   3.6671   3.5938   3.6855
  1  12.2199  11.8369  12.2182  11.1364  11.2517  11.3582  10.3571
  2  21.9087  21.5191  22.2821  23.3540  23.4949  23.8359  22.6605
  3  39.8665  39.8577  39.8581  39.8589  39.9450  39.9022  39.8729
  4  59.4650  59.5206  59.5342  59.6126  59.4119  59.4473  59.6309
  5  96.8981  96.9763  98.2184  97.2632  97.0063  90.7870  95.3015
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0   3.8265   3.6447   3.5962   3.6719   3.3923   3.5960   3.4958
  1  11.5338  11.2399  11.4651  11.0524  12.0171  10.3765  11.9160
  2  22.4437  23.0644  23.0044  22.3872  22.4847  23.0936  22.2746
  3  39.8577  39.8595  39.8580  39.8577  39.8594  39.8577  39.8577
  4  59.2656  59.4337  59.3434  59.5623  59.3891  59.4809  59.4462
  5  93.4997  94.9301 101.2173  98.6765  97.2858  96.5135 101.1185
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0   3.4734   3.5666   3.6360   3.6650   3.7264   3.5303   3.6512
  1  12.2873  10.8433  11.3771  11.0168  10.8262  11.1516  11.5637
  2  22.3000  23.2649  22.3917  22.2528  23.1594  23.0692  22.5232
  3  39.8578  39.8592  39.8591  39.8610  39.8596  39.8585  39.8584
  4  59.5315  59.2984  59.3724  59.4296  59.1306  58.9226  59.1892
  5 101.1966 100.5098  93.5758  91.6229  94.3420  99.0956  99.7293
   year
age 2013    
  0   3.5458
  1  11.8368
  2  22.4708
  3  39.8625
  4  59.2671
  5  97.9790

units:  NA 

Slot "discards":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997
  all 0    0    0    0    0    0    0    0    0    0    0    0    0   
     year
age   1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
  all 0    0    0    0    0    0    0    0    0    0    0    0    0   
     year
age   2011 2012 2013
  all 0    0    0   

units:  NA 

Slot "discards.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  1 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  2 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  3 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  4 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  5 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  1 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  2 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  3 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  4 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  5 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
   year
age 2013
  0 0   
  1 0   
  2 0   
  3 0   
  4 0   
  5 0   

units:  NA 

Slot "discards.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985    1986    1987    1988    1989    1990    1991    1992   
  0  3.6532  3.4611  4.1852  4.7990  3.5240  3.5432  3.5686  3.5737
  1 11.3859 11.4094 10.7864 10.9208 11.4493 11.3028 11.4519 12.2199
  2 23.2197 23.5354 23.5257 22.7368 22.6423 23.1079 23.4560 21.9087
  3 39.8577 39.8580 39.8599 40.2500 39.9222 39.8653 40.0094 39.8665
  4 59.3496 59.6720 60.0047 59.5889 59.7872 59.4888 59.4173 59.4650
  5  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
   year
age 1993    1994    1995    1996    1997    1998    1999    2000   
  0  3.7333  3.6320  3.5368  3.6671  3.5938  3.6855  3.8265  3.6447
  1 11.8369 12.2182 11.1364 11.2517 11.3582 10.3571 11.5338 11.2399
  2 21.5191 22.2821 23.3540 23.4949 23.8359 22.6605 22.4437 23.0644
  3 39.8577 39.8581 39.8589 39.9450 39.9022 39.8729 39.8577 39.8595
  4 59.5206 59.5342 59.6126 59.4119 59.4473 59.6309 59.2656 59.4337
  5  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
   year
age 2001    2002    2003    2004    2005    2006    2007    2008   
  0  3.5962  3.6719  3.3923  3.5960  3.4958  3.4734  3.5666  3.6360
  1 11.4651 11.0524 12.0171 10.3765 11.9160 12.2873 10.8433 11.3771
  2 23.0044 22.3872 22.4847 23.0936 22.2746 22.3000 23.2649 22.3917
  3 39.8580 39.8577 39.8594 39.8577 39.8577 39.8578 39.8592 39.8591
  4 59.3434 59.5623 59.3891 59.4809 59.4462 59.5315 59.2984 59.3724
  5  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
   year
age 2009    2010    2011    2012    2013   
  0  3.6650  3.7264  3.5303  3.6512  3.5458
  1 11.0168 10.8262 11.1516 11.5637 11.8368
  2 22.2528 23.1594 23.0692 22.5232 22.4708
  3 39.8610 39.8596 39.8585 39.8584 39.8625
  4 59.4296 59.1306 58.9226 59.1892 59.2671
  5  0.0000  0.0000  0.0000  0.0000  0.0000

units:  NA 

Slot "landings":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985  1986  1987  1988  1989  1990  1991  1992  1993  1994  1995 
  all 15292 16765 18320 20365 17762 16018 15746 14709 13265 16082 13015
     year
age   1996  1997  1998  1999  2000  2001  2002  2003  2004  2005  2006 
  all 12053 14693 14369 13699 15569 15006 12814 15674 14405 14601 14893
     year
age   2007  2008  2009  2010  2011  2012  2013 
  all 14227 12164 11840 13430 11423  9888 11254

units:  NA 

Slot "landings.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985    1986    1987    1988    1989    1990    1991    1992   
  0  28.242  23.026  59.863  87.583  85.120  24.241  37.785  64.576
  1 136.249  97.223 143.828 251.937 198.807 245.874 174.984 183.301
  2 123.464 164.965 122.299 154.170 158.743 264.890 183.578 199.169
  3  80.758  79.100  82.774  87.777  90.329  78.250  95.343  64.861
  4  43.094  44.479  61.249  66.955  55.246  24.141  35.914  30.297
  5  51.689  60.082  68.676  61.586  45.683  23.961  32.666  33.308
   year
age 1993    1994    1995    1996    1997    1998    1999    2000   
  0  57.788  68.150  68.078  37.792  33.533  58.288  37.498  17.538
  1 250.042 215.968 244.803 179.192 158.290 246.861 179.594 211.476
  2 176.138 224.500 153.038 149.822 184.718 146.685 144.680 169.683
  3  51.152  70.369  56.648  68.404  88.963  58.984  69.426  80.395
  4  23.242  26.086  22.841  22.853  39.951  32.727  35.523  37.796
  5  27.114  36.020  26.344  21.687  24.210  39.081  33.797  37.307
   year
age 2001    2002    2003    2004    2005    2006    2007    2008   
  0  28.657  19.958  58.022  66.847  19.269  33.028  27.082  15.925
  1 197.246 299.699 227.069 248.912 238.277 174.597 276.103 286.693
  2 185.113 190.989 244.351 162.812 182.680 178.085 147.444 163.687
  3  84.975  48.805  78.228  68.060  67.495  63.710  69.903  61.353
  4  29.106  17.499  29.984  31.323  28.467  30.916  31.339  21.385
  5  29.979  20.505  21.683  31.797  30.265  39.870  28.437  14.084
   year
age 2009    2010    2011    2012    2013   
  0  13.939  30.301  93.302  24.092   4.295
  1 190.718 155.590 127.894 119.511 138.311
  2 140.944 125.927 119.679  85.382 147.900
  3  59.636  82.183  75.960  44.170  53.653
  4  32.426  42.514  24.176  20.804  24.865
  5  21.934  29.184  22.413  26.463  25.440

units:  NA 

Slot "landings.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0   3.6532   3.4611   4.1852   4.7990   3.5240   3.5432   3.5686
  1  11.3859  11.4094  10.7864  10.9208  11.4493  11.3028  11.4519
  2  23.2197  23.5354  23.5257  22.7368  22.6423  23.1079  23.4560
  3  39.8577  39.8580  39.8599  40.2500  39.9222  39.8653  40.0094
  4  59.3496  59.6720  60.0047  59.5889  59.7872  59.4888  59.4173
  5  92.3146  93.0339  93.7232  95.3473  95.1656  92.8173  96.0019
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0   3.5737   3.7333   3.6320   3.5368   3.6671   3.5938   3.6855
  1  12.2199  11.8369  12.2182  11.1364  11.2517  11.3582  10.3571
  2  21.9087  21.5191  22.2821  23.3540  23.4949  23.8359  22.6605
  3  39.8665  39.8577  39.8581  39.8589  39.9450  39.9022  39.8729
  4  59.4650  59.5206  59.5342  59.6126  59.4119  59.4473  59.6309
  5  96.8981  96.9763  98.2184  97.2632  97.0063  90.7870  95.3015
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0   3.8265   3.6447   3.5962   3.6719   3.3923   3.5960   3.4958
  1  11.5338  11.2399  11.4651  11.0524  12.0171  10.3765  11.9160
  2  22.4437  23.0644  23.0044  22.3872  22.4847  23.0936  22.2746
  3  39.8577  39.8595  39.8580  39.8577  39.8594  39.8577  39.8577
  4  59.2656  59.4337  59.3434  59.5623  59.3891  59.4809  59.4462
  5  93.4997  94.9301 101.2173  98.6765  97.2858  96.5135 101.1185
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0   3.4734   3.5666   3.6360   3.6650   3.7264   3.5303   3.6512
  1  12.2873  10.8433  11.3771  11.0168  10.8262  11.1516  11.5637
  2  22.3000  23.2649  22.3917  22.2528  23.1594  23.0692  22.5232
  3  39.8578  39.8592  39.8591  39.8610  39.8596  39.8585  39.8584
  4  59.5315  59.2984  59.3724  59.4296  59.1306  58.9226  59.1892
  5 101.1966 100.5098  93.5758  91.6229  94.3420  99.0956  99.7293
   year
age 2013    
  0   3.5458
  1  11.8368
  2  22.4708
  3  39.8625
  4  59.2671
  5  97.9790

units:  NA 

Slot "stock":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997
  all NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA  
     year
age   1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
  all NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA  
     year
age   2011 2012 2013
  all NA   NA   NA  

units:  NA * NA 

Slot "stock.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0  756.814  764.447  969.811 1125.211  971.469  803.596  832.919
  1  807.439  594.133  605.087  740.002  842.246  718.610  636.044
  2  564.924  538.417  398.900  366.130  380.030  510.877  367.961
  3  330.052  351.499  292.807  216.862  161.904  169.180  182.225
  4  176.123  197.650  216.665  165.417   99.021   52.192   68.639
  5  211.249  266.985  242.937  152.154   81.881   51.804   62.432
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0 1010.470  919.021 1005.025  907.392  798.066  905.830  885.349
  1  647.833  769.041  700.291  761.362  681.501  619.293  711.360
  2  363.619  365.836  405.408  379.588  403.797  397.007  364.825
  3  137.551  120.435  142.345  132.153  173.856  196.423  160.115
  4   64.249   54.718   52.869   53.778   57.555   81.121   81.351
  5   70.633   63.834   73.001   62.027   54.620   49.158   97.146
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0  872.648  892.445 1105.914  888.587  998.293  989.508  787.866
  1  672.275  680.618  714.835  879.572  709.492  764.978  749.833
  2  361.173  389.111  367.523  408.142  451.489  377.226  403.097
  3  167.449  166.246  166.922  135.853  163.647  152.104  163.311
  4   78.261   75.002   64.376   60.914   67.503   64.168   63.726
  5   74.459   74.033   66.308   71.376   48.815   65.137   67.750
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0  968.876  942.771  779.478  685.701  651.320  864.234  752.294
  1  627.652  763.433  747.424  623.803  548.818  505.908  623.470
  2  400.189  357.108  377.703  355.278  339.607  309.650  299.293
  3  166.850  168.531  160.497  162.928  164.748  165.267  146.387
  4   73.339   79.566   75.462   76.475   79.977   61.596   67.474
  5   94.579   72.198   49.698   51.731   54.899   57.102   85.826
   year
age 2013    
  0  680.415
  1  594.176
  2  402.919
  3  168.390
  4   80.216
  5   82.073

units:  NA 

Slot "stock.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0   3.6532   3.4611   4.1852   4.7990   3.5240   3.5432   3.5686
  1  11.3859  11.4094  10.7864  10.9208  11.4493  11.3028  11.4519
  2  23.2197  23.5354  23.5257  22.7368  22.6423  23.1079  23.4560
  3  39.8577  39.8580  39.8599  40.2500  39.9222  39.8653  40.0094
  4  59.3496  59.6720  60.0047  59.5889  59.7872  59.4888  59.4173
  5  92.3146  93.0339  93.7232  95.3473  95.1656  92.8173  96.0019
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0   3.5737   3.7333   3.6320   3.5368   3.6671   3.5938   3.6855
  1  12.2199  11.8369  12.2182  11.1364  11.2517  11.3582  10.3571
  2  21.9087  21.5191  22.2821  23.3540  23.4949  23.8359  22.6605
  3  39.8665  39.8577  39.8581  39.8589  39.9450  39.9022  39.8729
  4  59.4650  59.5206  59.5342  59.6126  59.4119  59.4473  59.6309
  5  96.8981  96.9763  98.2184  97.2632  97.0063  90.7870  95.3015
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0   3.8265   3.6447   3.5962   3.6719   3.3923   3.5960   3.4958
  1  11.5338  11.2399  11.4651  11.0524  12.0171  10.3765  11.9160
  2  22.4437  23.0644  23.0044  22.3872  22.4847  23.0936  22.2746
  3  39.8577  39.8595  39.8580  39.8577  39.8594  39.8577  39.8577
  4  59.2656  59.4337  59.3434  59.5623  59.3891  59.4809  59.4462
  5  93.4997  94.9301 101.2173  98.6765  97.2858  96.5135 101.1185
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0   3.4734   3.5666   3.6360   3.6650   3.7264   3.5303   3.6512
  1  12.2873  10.8433  11.3771  11.0168  10.8262  11.1516  11.5637
  2  22.3000  23.2649  22.3917  22.2528  23.1594  23.0692  22.5232
  3  39.8578  39.8592  39.8591  39.8610  39.8596  39.8585  39.8584
  4  59.5315  59.2984  59.3724  59.4296  59.1306  58.9226  59.1892
  5 101.1966 100.5098  93.5758  91.6229  94.3420  99.0956  99.7293
   year
age 2013    
  0   3.5458
  1  11.8368
  2  22.4708
  3  39.8625
  4  59.2671
  5  97.9790

units:  Tonnes 

Slot "m":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  1 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  2 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  3 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  4 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  5 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  1 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  2 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  3 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  4 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  5 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
   year
age 2013
  0 0.2 
  1 0.2 
  2 0.2 
  3 0.2 
  4 0.2 
  5 0.2 

units:  NA 

Slot "mat":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  1 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  2 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
  5 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  1 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  2 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
  5 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
   year
age 2013
  0 0.0 
  1 0.0 
  2 0.0 
  3 0.5 
  4 1.0 
  5 1.0 

units:  NA 

Slot "harvest":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985      1986      1987      1988      1989      1990      1991     
  0 0.0420143 0.0337797 0.0704490 0.0896538 0.1014912 0.0338293 0.0513026
  1 0.2052350 0.1983939 0.3023849 0.4664010 0.2999438 0.4693404 0.3591603
  2 0.2744850 0.4091177 0.4094468 0.6159855 0.6092892 0.8308849 0.7839817
  3 0.3127523 0.2838539 0.3710438 0.5839320 0.9320718 0.7021002 0.8424810
  4 0.3127527 0.2838544 0.3710447 0.5839342 0.9320786 0.7021110 0.8425076
  5 0.3127527 0.2838544 0.3710447 0.5839342 0.9320786 0.7021110 0.8425076
   year
age 1992      1993      1994      1995      1996      1997      1998     
  0 0.0730271 0.0718121 0.0776586 0.0862769 0.0536127 0.0416721 0.0753142
  1 0.3714468 0.4402502 0.4124097 0.4341965 0.3403420 0.3291610 0.4778235
  2 0.9049974 0.7439321 0.9209337 0.5808594 0.5206431 0.7080658 0.5787399
  3 0.7218036 0.6232880 0.7733884 0.6312107 0.5622820 0.6814944 0.5158389
  4 0.7218503 0.6233622 0.7711998 0.6232826 0.5691329 0.7690638 0.5791774
  5 0.7218503 0.6233622 0.7711998 0.6232826 0.5691329 0.7690638 0.5791774
   year
age 1999      2000      2001      2002      2003      2004      2005     
  0 0.0485310 0.0219126 0.0289925 0.0250833 0.0662000 0.0773572 0.0273431
  1 0.3468038 0.4162142 0.3604376 0.4668834 0.4317032 0.4406712 0.4279124
  2 0.5758847 0.6463403 0.7952134 0.7139015 0.8879881 0.6371872 0.6820782
  3 0.6031630 0.7487315 0.8080579 0.4994079 0.7362098 0.6699664 0.6005665
  4 0.6835825 0.7958087 0.6798158 0.3783064 0.6631352 0.7590979 0.6684003
  5 0.6835825 0.7958087 0.6798158 0.3783064 0.6631352 0.7590979 0.6684003
   year
age 2006      2007      2008      2009      2010      2011      2012     
  0 0.0383116 0.0321901 0.0227904 0.0226745 0.0526466 0.1265433 0.0359512
  1 0.3639476 0.5037166 0.5437324 0.4080468 0.3723236 0.3249322 0.2365645
  2 0.6648206 0.5997648 0.6408010 0.5684835 0.5202251 0.5491893 0.3751396
  3 0.5405122 0.6034897 0.5413093 0.5115738 0.7838270 0.6958268 0.4015330
  4 0.6169215 0.5630756 0.3721444 0.6218329 0.8634098 0.5604856 0.4123003
  5 0.6169215 0.5630756 0.3721444 0.6218329 0.8634098 0.5604856 0.4123003
   year
age 2013     
  0 0.0069881
  1 0.2951425
  2 0.5134540
  3 0.4293282
  4 0.4149990
  5 0.4149990

units:  f 

Slot "harvest.spwn":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 2013
  0 0.5 
  1 0.5 
  2 0.5 
  3 0.5 
  4 0.5 
  5 0.5 

units:  prop 

Slot "m.spwn":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 2013
  0 0.5 
  1 0.5 
  2 0.5 
  3 0.5 
  4 0.5 
  5 0.5 

units:  NA 

Slot "name":
[1] "Swordfish MED                                      "

Slot "desc":
[1] "Imported from a VPA file. ( /home/laurie/Desktop/MEGAsync/mse/trade-offs/inputs/swo.idx ).  Thu Mar 26 08:54:50 2015 + FLAssess:  + FLAssess: "

Slot "range":
      min       max plusgroup   minyear   maxyear   minfbar   maxfbar 
        0         5         5      1985      2013         2         4 

Table 4a. XSA diagnostics from continuity run.

FLR XSA Diagnostics 2015-03-26 09:00:31

CPUE data from indices

Catch data for 29 years 1985 to 2013. Ages 0 to 5.

              fleet first age last age first year last year alpha beta
1 Moroccan Longline         2        4       1999      2011  <NA> <NA>
2  Spanish Longline         2        4       1988      2013  <NA> <NA>
3  Scilian Longline         2        4       1991      2009  <NA> <NA>
4   Scilian Gillnet         2        4       1990      2009  <NA> <NA>
5    Greek Longline         2        4       1987      2013  <NA> <NA>
6 Ligurian Longline         2        4       1991      2009  <NA> <NA>


 Time series weights :

    Tapered time weighting applied
   Power =   3 over  20 years

 Catchability analysis :

     Catchability independent of size for ages >   1 

     Catchability independent of age for ages >   4 

 Terminal population estimation :

     Survivor estimates shrunk towards the mean F
    of the final   5 years or the  1 oldest ages.

    S.E. of the mean to which the estimates are shrunk =   0.5 
 
    Minimum standard error for population
    estimates derived from each fleet =  0.3 

    prior weighting not applied

Regression weights
     year
age    2004 2005  2006  2007  2008  2009 2010  2011 2012 2013
  all 0.751 0.82 0.877 0.921 0.954 0.976 0.99 0.997    1    1


 Fishing mortalities
   year
age  2004  2005  2006  2007  2008  2009  2010  2011  2012  2013
  0 0.077 0.027 0.038 0.032 0.023 0.023 0.053 0.127 0.036 0.007
  1 0.441 0.428 0.364 0.504 0.544 0.408 0.372 0.325 0.237 0.295
  2 0.637 0.682 0.665 0.600 0.641 0.568 0.520 0.549 0.375 0.513
  3 0.670 0.601 0.541 0.603 0.541 0.512 0.784 0.696 0.402 0.429
  4 0.759 0.668 0.617 0.563 0.372 0.622 0.863 0.560 0.412 0.415
  5 0.759 0.668 0.617 0.563 0.372 0.622 0.863 0.560 0.412 0.415


 XSA population number (Thousand)
      age
year     0   1   2   3  4  5
  2004 990 765 377 152 64 65
  2005 788 750 403 163 64 68
  2006 969 628 400 167 73 95
  2007 943 763 357 169 80 72
  2008 779 747 378 160 75 50
  2009 686 624 355 163 76 52
  2010 651 549 340 165 80 55
  2011 864 506 310 165 62 57
  2012 752 623 299 146 67 86
  2013 680 594 403 168 80 82


 Estimated population abundance at 1st Jan  2014 
      age
year   0   1   2   3  4  5
  2014 0 553 362 198 90 43


 Fleet:  Moroccan Longline 

 Log catchability residuals.

   year
age   1999  2000   2001   2002   2003   2004  2005  2006   2007  2008
  2  0.012 0.103 -0.211 -0.089 -0.268 -0.002 0.142 0.076  0.115 0.168
  3 -0.035 0.170 -0.244  0.090 -0.145  0.093 0.183 0.069  0.040 0.153
  4 -0.064 0.161 -0.170  0.014 -0.114  0.170 0.329 0.100 -0.051 0.008
   year
age   2009   2010   2011
  2 -0.021 -0.066 -0.071
  3 -0.094 -0.057 -0.207
  4 -0.114 -0.125 -0.103


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -1.4740 -0.6464 0.1778
S.E_Logq   0.1375  0.1375 0.1375


 Fleet:  Spanish Longline 

 Log catchability residuals.

   year
age   1988   1989   1990   1991   1992   1993  1994   1995   1996   1997
  2  0.211 -0.178 -0.259 -0.158 -0.308 -0.062 0.017 -0.123 -0.402 -0.283
  3 -0.098 -0.008 -0.027 -0.250 -0.231  0.179 0.184  0.135 -0.359 -0.409
  4 -0.641 -0.330  0.336 -0.087 -0.284  0.155 0.360  0.217 -0.065 -0.302
   year
age   1998   1999   2000   2001   2002   2003   2004   2005   2006  2007
  2 -0.205 -0.305 -0.355 -0.301 -0.083 -0.458 -0.490 -0.257 -0.065 0.219
  3 -0.228 -0.343 -0.280 -0.325  0.105 -0.325 -0.387 -0.207 -0.063 0.153
  4 -0.337 -0.362 -0.278 -0.240  0.039 -0.284 -0.299 -0.051 -0.021 0.072
   year
age  2008  2009  2010  2011  2012   2013
  2 0.401 0.119 0.158 0.308 0.369 -0.077
  3 0.395 0.055 0.176 0.181 0.277 -0.061
  4 0.261 0.046 0.118 0.295 0.243 -0.139


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -0.9738 -0.1551 0.6586
S.E_Logq   0.2488  0.2488 0.2488


 Fleet:  Scilian Longline 

 Log catchability residuals.

   year
age   1991  1992 1993   1994  1995 1996   1997  1998  1999   2000  2001
  2 -0.001 0.043   NA -0.050 0.095   NA -0.387 0.161 0.341 -0.187 0.366
  3 -0.115 0.097   NA  0.094 0.330   NA -0.537 0.115 0.280 -0.134 0.320
  4  0.043 0.040   NA  0.266 0.408   NA -0.434 0.002 0.257 -0.137 0.400
   year
age  2002   2003  2004  2005  2006   2007   2008   2009
  2 0.580 -0.361 0.015 0.070 0.202 -0.263 -0.231 -0.070
  3 0.746 -0.251 0.096 0.097 0.182 -0.351 -0.260 -0.157
  4 0.675 -0.215 0.178 0.249 0.219 -0.437 -0.399 -0.171


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -0.8469 -0.0055 0.8129
S.E_Logq   0.2923  0.2923 0.2923


 Fleet:  Scilian Gillnet 

 Log catchability residuals.

   year
age   1990  1991  1992  1993  1994  1995   1996  1997   1998  1999  2000
  2 -0.268 0.206 0.811 0.480 0.133 0.490 -0.050 0.457  0.159 0.395 0.512
  3 -0.044 0.106 0.880 0.713 0.292 0.740 -0.015 0.323  0.128 0.349 0.579
  4  0.295 0.245 0.804 0.665 0.444 0.798  0.256 0.407 -0.005 0.307 0.557
   year
age  2001 2002 2003  2004  2005  2006 2007   2008   2009
  2 0.499   NA   NA 0.554 0.280 1.214   NA -0.973 -1.456
  3 0.467   NA   NA 0.650 0.321 1.209   NA -0.987 -1.528
  4 0.528   NA   NA 0.713 0.454 1.226   NA -1.145 -1.561


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3       4
Mean_Logq -3.3793 -2.5526 -1.7152
S.E_Logq   0.6471  0.6471  0.6471


 Fleet:  Greek Longline 

 Log catchability residuals.

   year
age   1987   1988 1989   1990  1991   1992  1993  1994   1995 1996 1997
  2 -0.149  0.192   NA -0.152 0.435 -0.414 0.101 0.351 -0.214   NA   NA
  3 -0.677 -0.117   NA  0.080 0.343 -0.338 0.341 0.517  0.043   NA   NA
  4 -1.187 -0.658   NA  0.444 0.508 -0.388 0.319 0.695  0.127   NA   NA
   year
age  1998  1999   2000  2001   2002   2003   2004   2005   2006   2007
  2 0.475 0.212 -0.074 0.097 -0.260 -0.090 -0.008 -0.075 -0.019  0.122
  3 0.451 0.173  0.001 0.072 -0.072  0.042  0.095 -0.027 -0.018  0.055
  4 0.345 0.157  0.005 0.159 -0.136  0.085  0.184  0.132  0.027 -0.023
   year
age   2008   2009  2010   2011   2012  2013
  2  0.020 -0.088 0.108 -0.036 -0.087 0.098
  3  0.013 -0.153 0.125 -0.164 -0.180 0.114
  4 -0.119 -0.160 0.069 -0.047 -0.212 0.038


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.7552 0.0646 0.8757
S.E_Logq   0.2873 0.2873 0.2873


 Fleet:  Ligurian Longline 

 Log catchability residuals.

   year
age   1991   1992   1993   1994   1995   1996   1997   1998   1999   2000
  2 -0.359 -0.588 -0.622 -0.375 -0.410 -0.501 -0.334  0.056 -0.288 -0.053
  3 -0.473 -0.534 -0.404 -0.231 -0.174 -0.481 -0.483  0.010 -0.349  0.000
  4 -0.317 -0.593 -0.435 -0.062 -0.099 -0.193 -0.382 -0.106 -0.374 -0.005
   year
age  2001   2002  2003   2004   2005   2006  2007  2008   2009
  2 0.366 -0.031 0.023 -0.335 -0.584 -0.147 0.590 0.410 -0.083
  3 0.319  0.135 0.133 -0.254 -0.557 -0.168 0.501 0.381 -0.170
  4 0.398  0.062 0.167 -0.174 -0.407 -0.133 0.414 0.240 -0.186


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.6145 0.2270 1.0475
S.E_Logq   0.3142 0.3142 0.3142


 Terminal year survivor and F summaries: 
 
 ,Age 0 Year class =2013 

source 
     scaledWts survivors yrcls
fshk     0.081        72  2013
nshk     0.919       662  2013

 ,Age 1 Year class =2012 

source 
     scaledWts survivors yrcls
fshk         1       271  2012

 ,Age 2 Year class =2011 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.365       183  2011
Greek Longline       0.397       218  2011
fshk                 0.239       189  2011

 ,Age 3 Year class =2010 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.392        84  2010
Greek Longline       0.392       101  2010
fshk                 0.217        60  2010

 ,Age 4 Year class =2009 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.393        38  2009
Greek Longline       0.393        45  2009
fshk                 0.214        42  2009

Table 4b. XSA diagnostics from alternative run.

FLR XSA Diagnostics 2015-03-26 09:00:33

CPUE data from indices

Catch data for 29 years 1985 to 2013. Ages 0 to 5.

              fleet first age last age first year last year alpha beta
1 Moroccan Longline         2        4       1999      2011  <NA> <NA>
2  Spanish Longline         2        4       1988      2013  <NA> <NA>
3  Scilian Longline         2        4       1991      2009  <NA> <NA>
4   Scilian Gillnet         2        4       1990      2009  <NA> <NA>
5    Greek Longline         2        4       1987      2013  <NA> <NA>
6 Ligurian Longline         2        4       1991      2009  <NA> <NA>


 Time series weights :

    Tapered time weighting applied
   Power =   3 over  20 years

 Catchability analysis :

     Catchability independent of size for ages >   1 

     Catchability independent of age for ages >   4 

 Terminal population estimation :

     Survivor estimates shrunk towards the mean F
    of the final   5 years or the  1 oldest ages.

    S.E. of the mean to which the estimates are shrunk =   0.5 
 
    Minimum standard error for population
    estimates derived from each fleet =  0.3 

    prior weighting not applied

Regression weights
     year
age    2004 2005  2006  2007  2008  2009 2010  2011 2012 2013
  all 0.751 0.82 0.877 0.921 0.954 0.976 0.99 0.997    1    1


 Fishing mortalities
   year
age  2004  2005  2006  2007  2008  2009  2010  2011  2012  2013
  0 0.077 0.027 0.038 0.032 0.023 0.023 0.053 0.127 0.036 0.007
  1 0.441 0.428 0.364 0.504 0.544 0.408 0.372 0.325 0.237 0.295
  2 0.637 0.682 0.665 0.600 0.641 0.568 0.520 0.549 0.375 0.513
  3 0.670 0.601 0.541 0.603 0.541 0.512 0.784 0.696 0.402 0.429
  4 0.759 0.668 0.617 0.563 0.372 0.622 0.863 0.560 0.412 0.415
  5 0.759 0.668 0.617 0.563 0.372 0.622 0.863 0.560 0.412 0.415


 XSA population number (Thousand)
      age
year     0   1   2   3  4  5
  2004 990 765 377 152 64 65
  2005 788 750 403 163 64 68
  2006 969 628 400 167 73 95
  2007 943 763 357 169 80 72
  2008 779 747 378 160 75 50
  2009 686 624 355 163 76 52
  2010 651 549 340 165 80 55
  2011 864 506 310 165 62 57
  2012 752 623 299 146 67 86
  2013 680 594 403 168 80 82


 Estimated population abundance at 1st Jan  2014 
      age
year   0   1   2   3  4  5
  2014 0 553 362 198 90 43


 Fleet:  Moroccan Longline 

 Log catchability residuals.

   year
age   1999  2000   2001   2002   2003   2004  2005  2006   2007  2008
  2  0.012 0.103 -0.211 -0.089 -0.268 -0.002 0.142 0.076  0.115 0.168
  3 -0.035 0.170 -0.244  0.090 -0.145  0.093 0.183 0.069  0.040 0.153
  4 -0.064 0.161 -0.170  0.014 -0.114  0.170 0.329 0.100 -0.051 0.008
   year
age   2009   2010   2011
  2 -0.021 -0.066 -0.071
  3 -0.094 -0.057 -0.207
  4 -0.114 -0.125 -0.103


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -1.4740 -0.6464 0.1778
S.E_Logq   0.1375  0.1375 0.1375


 Fleet:  Spanish Longline 

 Log catchability residuals.

   year
age   1988   1989   1990   1991   1992   1993  1994   1995   1996   1997
  2  0.211 -0.178 -0.259 -0.158 -0.308 -0.062 0.017 -0.123 -0.402 -0.283
  3 -0.098 -0.008 -0.027 -0.250 -0.231  0.179 0.184  0.135 -0.359 -0.409
  4 -0.641 -0.330  0.336 -0.087 -0.284  0.155 0.360  0.217 -0.065 -0.302
   year
age   1998   1999   2000   2001   2002   2003   2004   2005   2006  2007
  2 -0.205 -0.305 -0.355 -0.301 -0.083 -0.458 -0.490 -0.257 -0.065 0.219
  3 -0.228 -0.343 -0.280 -0.325  0.105 -0.325 -0.387 -0.207 -0.063 0.153
  4 -0.337 -0.362 -0.278 -0.240  0.039 -0.284 -0.299 -0.051 -0.021 0.072
   year
age  2008  2009  2010  2011  2012   2013
  2 0.401 0.119 0.158 0.308 0.369 -0.077
  3 0.395 0.055 0.176 0.181 0.277 -0.061
  4 0.261 0.046 0.118 0.295 0.243 -0.139


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -0.9738 -0.1551 0.6586
S.E_Logq   0.2488  0.2488 0.2488


 Fleet:  Scilian Longline 

 Log catchability residuals.

   year
age   1991  1992 1993   1994  1995 1996   1997  1998  1999   2000  2001
  2 -0.001 0.043   NA -0.050 0.095   NA -0.387 0.161 0.341 -0.187 0.366
  3 -0.115 0.097   NA  0.094 0.330   NA -0.537 0.115 0.280 -0.134 0.320
  4  0.043 0.040   NA  0.266 0.408   NA -0.434 0.002 0.257 -0.137 0.400
   year
age  2002   2003  2004  2005  2006   2007   2008   2009
  2 0.580 -0.361 0.015 0.070 0.202 -0.263 -0.231 -0.070
  3 0.746 -0.251 0.096 0.097 0.182 -0.351 -0.260 -0.157
  4 0.675 -0.215 0.178 0.249 0.219 -0.437 -0.399 -0.171


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -0.8469 -0.0055 0.8129
S.E_Logq   0.2923  0.2923 0.2923


 Fleet:  Scilian Gillnet 

 Log catchability residuals.

   year
age   1990  1991  1992  1993  1994  1995   1996  1997   1998  1999  2000
  2 -0.268 0.206 0.811 0.480 0.133 0.490 -0.050 0.457  0.159 0.395 0.512
  3 -0.044 0.106 0.880 0.713 0.292 0.740 -0.015 0.323  0.128 0.349 0.579
  4  0.295 0.245 0.804 0.665 0.444 0.798  0.256 0.407 -0.005 0.307 0.557
   year
age  2001 2002 2003  2004  2005  2006 2007   2008   2009
  2 0.499   NA   NA 0.554 0.280 1.214   NA -0.973 -1.456
  3 0.467   NA   NA 0.650 0.321 1.209   NA -0.987 -1.528
  4 0.528   NA   NA 0.713 0.454 1.226   NA -1.145 -1.561


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3       4
Mean_Logq -3.3793 -2.5526 -1.7152
S.E_Logq   0.6471  0.6471  0.6471


 Fleet:  Greek Longline 

 Log catchability residuals.

   year
age   1987   1988 1989   1990  1991   1992  1993  1994   1995 1996 1997
  2 -0.149  0.192   NA -0.152 0.435 -0.414 0.101 0.351 -0.214   NA   NA
  3 -0.677 -0.117   NA  0.080 0.343 -0.338 0.341 0.517  0.043   NA   NA
  4 -1.187 -0.658   NA  0.444 0.508 -0.388 0.319 0.695  0.127   NA   NA
   year
age  1998  1999   2000  2001   2002   2003   2004   2005   2006   2007
  2 0.475 0.212 -0.074 0.097 -0.260 -0.090 -0.008 -0.075 -0.019  0.122
  3 0.451 0.173  0.001 0.072 -0.072  0.042  0.095 -0.027 -0.018  0.055
  4 0.345 0.157  0.005 0.159 -0.136  0.085  0.184  0.132  0.027 -0.023
   year
age   2008   2009  2010   2011   2012  2013
  2  0.020 -0.088 0.108 -0.036 -0.087 0.098
  3  0.013 -0.153 0.125 -0.164 -0.180 0.114
  4 -0.119 -0.160 0.069 -0.047 -0.212 0.038


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.7552 0.0646 0.8757
S.E_Logq   0.2873 0.2873 0.2873


 Fleet:  Ligurian Longline 

 Log catchability residuals.

   year
age   1991   1992   1993   1994   1995   1996   1997   1998   1999   2000
  2 -0.359 -0.588 -0.622 -0.375 -0.410 -0.501 -0.334  0.056 -0.288 -0.053
  3 -0.473 -0.534 -0.404 -0.231 -0.174 -0.481 -0.483  0.010 -0.349  0.000
  4 -0.317 -0.593 -0.435 -0.062 -0.099 -0.193 -0.382 -0.106 -0.374 -0.005
   year
age  2001   2002  2003   2004   2005   2006  2007  2008   2009
  2 0.366 -0.031 0.023 -0.335 -0.584 -0.147 0.590 0.410 -0.083
  3 0.319  0.135 0.133 -0.254 -0.557 -0.168 0.501 0.381 -0.170
  4 0.398  0.062 0.167 -0.174 -0.407 -0.133 0.414 0.240 -0.186


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.6145 0.2270 1.0475
S.E_Logq   0.3142 0.3142 0.3142


 Terminal year survivor and F summaries: 
 
 ,Age 0 Year class =2013 

source 
     scaledWts survivors yrcls
fshk     0.081        72  2013
nshk     0.919       662  2013

 ,Age 1 Year class =2012 

source 
     scaledWts survivors yrcls
fshk         1       271  2012

 ,Age 2 Year class =2011 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.365       183  2011
Greek Longline       0.397       218  2011
fshk                 0.239       189  2011

 ,Age 3 Year class =2010 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.392        84  2010
Greek Longline       0.392       101  2010
fshk                 0.217        60  2010

 ,Age 4 Year class =2009 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.393        38  2009
Greek Longline       0.393        45  2009
fshk                 0.214        42  2009